Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent nested hierarchy. The difference drawn here between "subjective" and "objective" is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically - perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999). Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese. The difference between classifying cars and classifying languages lies in the fact that, with cars, certain characters (for example, color or manufacturer) must be considered more important than other characters in order for the classification to work. Which types of car characters are more important depends upon the personal preference of the individual who is performing the classification. In other words, certain types of characters must be weighted subjectively in order to classify cars in nested hierarchies; cars do not fall into natural, unique, objective nested hierarchies.

Because of these facts, a cladistic analysis of cars will not produce a unique, consistent, well-supported tree that displays nested hierarchies. A cladistic analysis of cars (or, alternatively, a cladistic analysis of imaginary organisms with randomly assigned characters) will of course result in a phylogeny, but there will be a very large number of other phylogenies, many of them with very different topologies, that are as well-supported by the same data. In contrast, a cladistic analysis of organisms or languages will generally result in a well-supported nested hierarchy, without arbitrarily weighting certain characters (Ringe 1999). Cladistic analysis of a true genealogical process produces one or relatively few phylogenetic trees that are much more well-supported by the data than the other possible trees.

The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).

He also severely misunderstands convergence. Convergence can only produce functionally-relevant similarities, because that is all that selection can "see". Homologies, i.e. similarities between systems that are not necessary for functional similarity between systems, are what allows paleontologists to easily distinguish between these placental wolf and marsupial "wolf" skulls that cre8tionist posted in another thread:

Portrayed here are side-by-side images demonstrating the anatomical differences between the skulls of the Grey wolf (Canis lupus) and the thylacine (Thylacinus cynocephalus). In the dorsal view, note that the thylacine has a much broader forehead than the wolf, and there are differences in the design of the zygomatic arches and brain case. Also, the rostrum (snout) of the thylacine is far narrower than that of the wolf, and the thylacine has proportionately larger eye sockets which are rather more square in shape. In the ventral view, one can easily see the great differences in dentition that readily distinguish the two species as being members of distinct mammal groups. The dentition of both species will be represented in greater detail on the following page. Also visible in the ventral view is the thylacine's maxillary palatal vacuity (the two parallel openings in the roof of the mouth). This is a feature that the wolf and other placental mammals do not have.

Here I show some diagrams which I have prepared to illustrate the extreme difference in dental anatomy which exists between the thylacine and its placental counterpart, the wolf. The images are portrayed at life size. Although there are also a number of notable differences in post cranial skeletal structure between the thylacine and wolf, I felt that the dentition represented one of the most striking dissimilarities. As you can easily see in the image of the maxilla, the thylacine has 8 top incisors, whereas the wolf has only 6. In the mandible however, the thylacine and wolf have an equal number of incisors. Another major difference is the presence of a specialized shearing tooth, the carnassial, in the wolf. This tooth design is a trademark of the wolf and other members of the placental mammal family Carnivora. Also make note that unlike the wolf, the thylacine lacks large grinding surfaces on its molars. Altogether, the wolf has a complement of 42 teeth, and the thylacine 46.

I can't post the images here because they are copyright protected, but the differences in the tooth-numbering are dramatic.

All commonly-sighted cases of "uncanny convergence" in biology turn out, on investigation, to be externally impressive but superficial when you get down to details. This is notably different from the kinds of things that have happened in aircraft design, e.g. the addition of (the same) transponders, GPS units, computers, TV screens, etc., to planes of widely different models.

This has been pointed out many times over the years, so I'm not sure why these cases still get seriously cited.

yersinia

PS: There is also the interesting question of:

If the hypothesized IDer decided that there needed to be some carnivorous canine-type critters in Australia, why bother with all the genetic engineering that would be required, when a simple aboriginal boat sufficed to bring dingos to Australia only ~15,000 years ago?

Such ID puzzles are absolutely ubiquitous in biogeography. To me they indicate strongly that whatever creativity made these wonderful adaptations was, for some odd reason, highly constrained so that "design information" could not be transmitted across deep water barriers and instead had to be re-invented from scratch each time the adaptation was "needed" in particular locations. Strangely, such geographical constraints did not apply to flying birds, sea mammals, and other easily-dispersed organisms.

If you can find an ID theory that can explain this (and "the designer's actions are mysterious" is not an explanation), I'll eat my hat. If on the other hand you give natural selection the credit for these instances of creativity, then I guess natural selection can "design" things after all, and quite skillfully too...

You argue that designed objects will not produce nested hierarchies. I already gave the aircraft example, let's consider the example a bit further. Consider all machines that use gasoline as a fuel. Within that set you have various subsets, such as those that move and do not move. Of those that move, some fly, others move along the surface of the earth. In the latter, you have various numbers of wheels, such as 2, 4, 6, 8, …, and a few outliers with odd number of wheels. Of those with 4 wheels, you have different ratios of interior volume to overall size (eg, vans have a higher ratio). Of those with lower ratios you have different carburetors (fuel injection for sports cars), and so forth. I am contriving this example off the top of my head, but perhaps you can explain why this cannot be a case of a nested hierarchy. In support of your claim you pasted a few paragraphs from a web document which does not support your claim. The web document is discussing the relationships, across designed objects, of characters which have no influence on performance or are constant over the entire set. What we have called in this thread "arbitrary design decisions."

Did you even read the quote? The very first sentence pointed out that anything can be subjectively classified into a nested hierarchy if you arbitrarily pick characters. This is exactly what you do above. The point is that your "tree" would not be produced by an analysis of other subsystems of gasoline-driven machines, e.g. tires, liscense plates, GPS units, radios, onboard computers, whatever. On the other hand, in biology there are a large number of systems (genes, limbs, skulls, etc.) that produce highly-congruent nested trees. Other fairly similar examples are things like languages and scribe-copied documents, both of which are produced by a process of copying and gradual modification (although in these cases the possibility of lateral transfer is somewhat higher than it is in eukaryote biology).

As for web references, if they cite the primary literature then you either have to show they are mis-using the literature, or that the literature itself is wrong. Theobald cites a large number of papers discussing the difference between arbitrary and natural hierarchies -- designed objects like cars and planes produce the former, copied & gradually modified objects (like languages, scribe-copied documents, and...organisms) produce the latter.

I'll include some of Theobald's refs so that interested parties can look them up:

You seem to be extrapolating from the discussion given there on arbitrary design decisions to conclude that designed objects cannot produce nested hierarchies. Perhaps I am misunderstanding you.

Of course designed objects can produce just about anything, because a hypothetical designer can always be invented who wants to produce X for goodness-knows-what reason. This is a major problem for ID "theory", no predictions are made unless some specifications are put on the hypothetical IDer, and no one wants to even hypothesize any such specifications (you don't have to have foreknowledge of the designer, just a hypothesis...this is how science proceeds).

But you said that ID predicts congruent phylogenies. I am arguing that this is not established or even likely based on what we know about designed objects.

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Is there more than one cost function?

This section seems like you are trying to say something about how the designer would design things so that congruent phylogenies resulted due to functional constraints, or something. But what you have to explain, in order to explain things as well as current theory, is how all of those arbitrary characters (many of them, such as DNA degeneracy, absolutely known to be functionless differences) produce statistically the same nested hierarchical trees! If you can't do that then there's no reason to switch from the current explanation.

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Can homologies arise from different genes?

You next go on to discuss homologies, but I'm not sure what the point is. You state that paleontologists can easily distinguish between the placental wolf and marsupial wolf skulls, as though I had stated otherwise. Of course they can, they can also easily distinguish between the bat's wing and human hand, but this does not prevent the pentadactyl pattern from being claimed as evidence for evolution. You pasted a figure of the two skulls which appear highly similar yet are supposed to have evolved independently. You say the similarities are "superficial." I have heard this said many times before, but how is it that these similarities are superficial whereas homologies such as the pentadactyl pattern, which exhibit a large degree of variance (compare the porpoise, bat and horse) are significant?

Because the homologies all correlate with each other to a high degree of statistical confidence, producing a Linnean-type classification, whereas those features that you would expect would be the important features (as revealed by you example of classification of gas-driven machines based on function, or John Bracht's imaginings that amino acid sequence won't turn out to be largely degenerate with respect to structure and function after all) in fact don't correlate with the Linnean-type classification.

If the genes and proteins of penguins, sharks, dolphins, seals, etc. grouped together, and bats and birds grouped together, etc., then you'd have an argument, but they don't. This is a massive mystery from an ID perspective but easily explained by evolution.

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We should also note that homologies can develop from different genes, or otherwise follow different development patterns.

This is an argument of Wellsian origin and depends largely on obfuscatory use of quotes and words like "different" (and Wells' unique views about the unimportance of DNA, which are rebutted in detail this ISCID thread). Similar genes perform similar developmental functions a very long ways back, e.g. Hox genes and front-to-back patterning:

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An interesting challenge?

Finally, you issued a challenge which sounded interesting but, forgive me if I am slow this morning, I had trouble following. You wrote:

quote:--------------------------------------------------------------------------------If the hypothesized IDer decided that there needed to be some carnivorous canine-type critters in Australia, why bother with all the genetic engineering that would be required, when a simple aboriginal boat sufficed to bring dingos to Australia only ~15,000 years ago? -- Yersinia--------------------------------------------------------------------------------

Can you elaborate a bit?

In short:

You and Cre8tionist have proposed that convergences like the placental/marsupial wolf are better explained by intelligent design for the same function.

I pointed out that rather than the "same" design being transplanted, it looks more like it was independently invented by modification of different starting points, and that the convergence is superficial in that the true relationships of the organisms remain clear based on homologies.

But, if you are going to maintain the hypothesis that ID accounts for the complex carnivory specializations of wolves and thylacines, you have to explain why it appears that the design wasn't transplanted, but rather re-invented. If a designer wanted carnivores in Australia, it would have been much easier just to put some dogs on a boat, as the stone-age Aborigines did, rather than do all of that complex creative genetic engineering twice in two different ways.

Ditto for carnivorous marsupial "cats" in isolated south America, cacti vs. south African succulents, lemurs in Madagascar, Hawaiian honeycreepers, and of course Darwin's finches. Why should independent design correlate so well with geographical isolation? Did the IDer not know of boats?

Well, I am glad that Cornelius concedes that ID-design is different from regular design inferences, in that while we always have (even if approximate) models for the designer in the cases of forensics, archaeology, and even SETI, no such model shall be forthcoming for ID. Therefore we can expect nothing in particular if ID is true, and thus have no way to strengthen or weaken our confidence in the hypothesis.

I say this somewhat in jest, because Hunter in fact only uses the "there ain't no hypothetical model for the designer" argument as a defense, in fact he makes a few characterizations at times. Things have to "make sense" with regard to some unspecified criteria:

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With regard to the complex carnivory specializations you mention, ID is more interested in understanding the function and reason (or perhaps lack thereof) behind the different designs, not trying to justify the actions of the designer. So your challenge, as it stands, is fairly weak. To beef it up you need to show that those different specializations are unnecessary or absurd. As I said to RBH, the way to falsify design is:

1) Show that the designer's actions make little sense,2) Show that naturalistic mechanisms are sufficient to explain the origin of species,3) Show that the preponderance of scientific evidence/analysis strongly points to evolution.

Any of these is sufficient to falsify ID, or at least effectively falsify it by rendering ID redundant.

The "origin of species" is a somewhat different topic and can be address elsewhere; I expect that if the usual examples of observed speciation or inferred very-recent-speciation were cited, he would back up the goalposts to the level of genus, family, order, phylum, etc. But that's another thread.

I think, though, that #1 and #3 are pretty easily satisfied by the Thylacine example:

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Sarcastic and rhetorical barbs about how the designer didn't create according to your personal sensibilities will only backfire, but a serious and plausible challenge on #1 will work for you. For example, in this example you bring up, show that one of the specializations is unquestionably superior to the other, even if transplanted into those other species in that other environment and niche.

Well, how's this: the introduction of the dingo appears to have quite rapidly caused the extinction of the thylacine, which was extinct from mainland Australia before Europeans arrived. Thylacine species persisted for tens of millions of years in the Australian fossil record, into the period of human habitation, and yet some stone-age boat people (unintentionally) killed them off by transplanting an apparently superior design, the dingo.

The only place that thylacines hung on until the 1900's was in the isolated island of Tasmania, where dingos and bounty hunters reduced their population to fatally low numbers by the 1930's.

As if this wasn't enough, this appears to be a general pattern with only a few exceptions: placentals have proven to be superior competitors for the same ecological niches, which is why there are precious few marsupials in South America (formerly an Australia-like place before the Panamanian isthmus connected it to North America), and why so many marsupials are endangered in Australia, while things like feral rats, cats, rabbits, and dogs (dingo) are thriving wildly.

By any standard of "good design", it appears that the hypothetical IDer's actions "make little sense": to carefully craft all of these marsupial species for parallel ecological niches on separate landmasses, let them be fruitful and multiply for millions of years, followed by prompt extermination once tectonic accidents or stone-age boats allow apparently superior designs to invade.

It appears that the thread has devolved into several subtopics that are not strictly related to phylogenetic tree (non)congruence. Hunter's non-congruence reasons for why we should doubt the common descent of (say) Animalia appear to have been rebutted, as he is now raising numerous different issues that would take their own threads to address:

I think that these questions are perhaps the real reasons that Hunter doubts common descent of animal species, not because the phylogenetic evidence is against it.

I think that the thylacine example is worth cogitating on further regarding ID vs. evolution, as it is not an isolated event but rather an instance of a very common phenomenon in biology: in geographically isolated regions, relatively unrelated organisms adapt to fill quite specific niches, but do it by "reinvention" that always differs in the details. Information transplants are not seen.

I would humbly note that this is what Darwin realized about the Galapagos species of turtles (and later, finches) once the taxonomists got to work on them back in Britain. He and many other world travellers have made remarks like "it is as if different creators acted in different places" or words to that effect.

When convergent organisms are transplanted by humans or natural events, a very common occurence is extinction of the native species. It's almost like whatever the creative force is draws its power from the size and time of isolation of the land mass in question...